MicroRNAs (miRNAs), together with RNA binding proteins (RNABPs), constitute the primary regulators of eukaryotic posttranscriptional gene expression and function in a broad range of cellular processes. miRNAs are a large family of small noncoding RNAs (ncRNAs) that repress gene expression by affecting the stability or translation of target messenger RNAs (mRNAs) (1-3). The current understanding of global miRNA targeting of mRNAs is based upon computational predictions of complementary sequence elements that are refined by considering evolutionary homologies across multiple species (4). While these algorithms predict hundreds of potential mRNA targets per miRNA, it is not certain that each miRNA gains functional access to these target mRNAs in the cell under a given set of conditions. Indeed, recent evidence suggests that RNABPs can influence the regulatory fates of mRNAs targeted by miRNAs in a condition-dependent manner (5, 6).
RNABPs, among the largest protein families encoded in eukaryotic genomes, can regulate gene expression at multiple posttranscriptional levels (7, 8). Like miRNAs, RNABPs also function through binding specific RNA sequence motifs frequently contained within untranslated regions (UTRs) of target mRNAs. When occurring in the cytoplasmic compartment, these interactions may determine mRNA localization, stability and/or translational activation (9). It is becoming increasingly evident that the posttranscriptional infrastructure is highly organized and utilizes multiple cis-trans interactions to combinatorially regulate higher order gene expression (7, 10). Global exploration of the in vivo composition and organization of this posttranscriptional infrastructure has only recently begun. A number of studies have identified RNABPs associated with mRNA subsets that have similar metabolic fates or encode functionally related proteins (7). Several predicted functional interactions between miRNAs and mRNAs have been confirmed using reporter systems, while a number of primarily bioinformatics approaches have predicted the global targeting of a substantial proportion of all cellular mRNAs by miRNAs (2, 4; 11). While miRNAs are expected to act combinatorially on their mRNA targets, the composition and organization of endogenous miRNAs, mRNAs and RNABPs within messenger ribonucleoprotein (mRNP) complexes are poorly understood.